tbuckley/cabot-search huggingface dataset:
Abstract 127: Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models
Authors: Xuan C. Li, Yuelin Liu, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Malikić, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp
Journal: Cancer Research (2023)

Abstract Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression history of a tumor via single-cell lineage tree reconstruction. In this work, we introduce the first principled distance-based computational method, Sgootr, for inferring a tumor's single-cell methylation lineage tree and jointly identifying lineage-informative CpG sites which harbor changes in methylation status that are retained along the lineage. We apply Sgootr on the single-cell bisulfite-treated whole genome sequencing data of multiregionally-sampled tumor cells from 9 metastatic colorectal cancer patients made available by Bian et al., as well as multiregionally-sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient made available by Chaligne et al. We demonstrate that the tumor lineages constructed reveal a simple model underlying colorectal tumor progression and metastatic seeding. A comparison of Sgootr against alternative approaches shows that Sgootr can construct lineage trees with fewer migration events and more in concordance with the sequential-progression model of tumor evolution, in time a fraction of that used in prior studies. Interestingly, lineage-informative CpG sites identified by Sgootr are in inter-CpG island (CGI) regions, as opposed to CGI's, which have been the main regions of interest in genomic methylation-related analyses. Sgootr is implemented as a Snakemake workflow, available at https://github.com/liuy0421/Sgootr. Citation Format: Xuan C. Li, Yuelin Liu, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Malikić, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp. Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 127.
Abstract 4551: Reconstructing the metastatic tumor microenvironment of high grade serous ovarian cancer: understanding the contribution of malignant cells
Authors: Beatrice Malacrida, Samar Elorbany, Eleni Maniati, Florian Laforets, Ranjit Manchanda, Frances R. Balkwill
Journal: Cancer Research (2023)

Abstract Following a ‘deconstruction’ of the metastatic tumor microenvironment (TME) of high grade serous ovarian cancer (HGSOC), we developed 3-dimensional (3D) human multicellular in vitro models using patient-derived primary cells and HGSOC malignant cell lines. In this study, we used these 3D in vitro human models to study how malignant cells influence the surrounding TME. Using patient-derived primary adipocytes, fibroblasts and mesothelial cells isolated from macroscopically normal omentum (the primary site of metastasis in HGSOC) from women undergoing gynaeco-oncology surgery, we built multicellular models combining those cells with different high grade serous malignant cell lines and monocytes isolated from healthy individuals. We found that peripheral blood monocytes were able to differentiate and polarize to macrophages in our pentacultures (i.e., five different cell types) with phenotypes also found in HGSOC omental metastases. In addition, the cells in our pentaculture models self-rearranged in ways that were dependent on the HGSOC malignant cell lines used in the culture. Macrophage phenotype and cytokine secretion from the multicellular cultures was also influenced by the different malignant HGSOC cell lines used in the model. RNAseq analysis of the pentacultures showed that the cultures clustered according to the malignant cell line used. In addition, we were able to identify some gene expression clusters in the macrophages and fibroblasts of the pentacultures that matched those found by single cell RNAseq analysis of human HGSOC biopsies. These human 3D in vitro multicellular models allow us to define the contribution of each cell type to tumor growth and spread, and also provide us a semi-high throughput platform to investigate antibody or drug targets. Citation Format: Beatrice Malacrida, Samar Elorbany, Eleni Maniati, Florian Laforets, Ranjit Manchanda, Frances R. Balkwill. Reconstructing the metastatic tumor microenvironment of high grade serous ovarian cancer: understanding the contribution of malignant cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4551.
Abstract 1454: SMAD3 promotes expression and activity of the androgen receptor in prostate cancer
Authors: Hee-Young Jeon, Majid Pornour, Hyunju Ryu, Sudeep Khadka, Rui Xu, Jihyun Jang, Deqiang Li, Hegang Chen, Arif Hussain, Ladan Fazli, Martin Gleave, Xuesen Dong, Qianben Wang, Christopher Barbieri, Jianfei Qi
Journal: Cancer Research (2023)

Abstract Overexpression of the androgen receptor (AR) is the primary cause of development of castration-resistant prostate cancer (CRPC), although mechanisms upregulating AR transcription in this context are not well understood. Our RNA-seq analysis revealed AR as the top pathway altered after SMAD3 knockdown in prostate cancer cells. SMAD3 knockdown decreased levels of AR, AR-V7 and AR target gene transcripts, whereas SMAD4 or SMAD2 knockdown had little or no effect. ChIP-seq analysis showed that SMAD3 knockdown decreased global binding of AR to chromatin. Mechanistically, we show that SMAD3 binds to intron 3 of the AR gene to promote AR expression. Targeting these binding sites by CRISPRi reduced transcript levels of AR and AR targets. In addition, ~50% of AR or SMAD3 ChIP-seq peaks overlapped, and SMAD3 may also cooperate with or co-activate AR in terms of AR target expression. Functionally, AR re-expression in SMAD3-knockdown cells partially rescued AR target expression and cell growth defects. AR and SMAD3 mRNAs were upregulated in datasets of metastatic prostate cancer and CRPC compared with primary prostate cancer. This study suggests that SMAD3 could be targeted to downregulate AR expression and activity and as potential anti-prostate cancer therapy. Citation Format: Hee-Young Jeon, Majid Pornour, Hyunju Ryu, Sudeep Khadka, Rui Xu, Jihyun Jang, Deqiang Li, Hegang Chen, Arif Hussain, Ladan Fazli, Martin Gleave, Xuesen Dong, Qianben Wang, Christopher Barbieri, Jianfei Qi. SMAD3 promotes expression and activity of the androgen receptor in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1454.
Abstract 5807: mTOR regulates stem cells of glioblastoma by altering the self-renewal and proliferation
Authors: Olivia Gellerson, Julie Bree, Mohan Das, George Kleinman, Chirag Gandhi, Meena Jhanwar-Uniyal
Journal: Cancer Research (2023)

Abstract The mechanistic target of rapamycin (mTOR: aka mammalian target of rapamycin), a serine/threonine kinase, functions by forming two multiprotein complexes termed mTORC1 and mTORC2. Glioblastoma (GBM) is a malignant and lethal brain tumor that remains incurable partly due to the existence of untreatable cancer stem cells (CSC). The pathogenesis of GBM is largely due to the loss of the tumor suppressor gene PTEN, which is implicated in the aberrant activation of the mTOR pathway. The major cause of tumor recurrence, growth, and invasion is the presence of a unique population of CSC. Resistance to conventional therapies appears to be caused by both extensive genetic abnormalities and dysregulation of the transcription landscape. Consequently, CSCs have emerged as targets of interest in new treatment paradigms. Evidence suggests that inhibition of the mTOR pathway can also be applied to target CSCs. In this study, we explored the role of the mTOR pathway in the regulation of stem cells of GBM. GBM stem cells were treated with various inhibitors of canonical PI3K/AKT/mTOR pathways such as rapamycin (mTORC1 inhibitor), PP242 (ATP binding mTORC1/2 inhibitor), LY294002 (PI3K inhibitor), and MAPK inhibitor, U0126. We previously demonstrated the presence of CSC in the peritumor area of GBM. A significant number of GBM tumors expressed stem cell marker nestin and activated mTOR (pmTORSer2448), with most tumor cells co-expressing both markers. The expression of stem cell marker NANOG was suppressed following rapamycin treatment, while U0126 induced translocation of NANOG from the nucleus to the cytoplasm. The neurospheres were disrupted following rapamycin and LY294002 treatments. Rapamycin or PP242 treatments given with differentiating agent All-trans-retinoic acid reduced stem cell proliferation. Treatment with novel small molecule dual inhibitors of mTORC1/2 demonstrated that Torin1 and Torin2 suppressed the proliferation of GBM CSC, while XL388 was less effective. Torin1 and XL388 delay the process of self-renewal as compared to controls, whereas Torin2 halted the self-renewal of GBM CSC. Additionally, Torin2 was able to eradicate tumor cells. Torin2 effectively targeted CSCs of GBM by halting self-renewal and inhibiting cell proliferation, underscoring the use of Torin2 in the treatment of GBM. Citation Format: Olivia Gellerson, Julie Bree, Mohan Das, George Kleinman, Chirag Gandhi, Meena Jhanwar-Uniyal. mTOR regulates stem cells of glioblastoma by altering the self-renewal and proliferation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5807.
Abstract 388: Acquired sensitivity to ONC201/TIC10 in ER+ breast cancer progressing on the mTOR inhibitor everolimus
Authors: Eleni Farmaki, Rena Emond, Aritro Nath, Vince K. Grolmusz, Patrick A. Cosgrove, Andrea H. Bild
Journal: Cancer Research (2023)

Abstract The mTOR inhibitor everolimus has become an important component for clinical management of metastatic ER+ breast cancer. Despite the improved patient outcomes, progression and resistance will still develop. Therefore, it is important to research strategies that can increase response durability and effectiveness of this therapy. Here we developed everolimus resistance models and performed pre-clinical evaluation of the small molecule ONC201/TIC10, a drug candidate showing promising results in clinical trials with advanced cancer patients. ONC201/TIC10 targets mitochondrial function and metabolism and activates stress response, however its efficacy has not been studied in everolimus resistant breast cancer. Transcriptomic analysis in everolimus resistant tumors identified sustained mitochondrial oxidative phosphorylation activity suggesting increased sensitivity to ONC201/TIC10. Our results show that combination treatment of ONC201/TIC10 with everolimus inhibits the growth of sensitive as well as everolimus resistant cells in 2D and 3D in vitro studies. The increased response to combination therapy was confirmed in primary cells from patients progressing on endocrine and mTOR therapy, supporting clinical relevance. We further show that the mechanism of ONC201/TIC10 anti-proliferative activity involves disruption of mitochondrial function and increased levels of the pro-apoptotic transcription factors CHOP and ATF4. Importantly, several resistant cell lines demonstrated increased dependency on mitochondrial respiration compared to sensitive cells which contributes to a vulnerability to ONC201/TIC10. In conclusion, we used pre-clinical models to characterize acquired sensitivity to mTOR inhibition. Combining patient derived data with resistant cell line driven experiments, our study provides validated findings in various settings strengthening the potential for clinical applications of ONC201/TIC10. We propose that ONC201/TIC10 and modulation of mitochondrial function is effective in drug resistant cancer cells and can enhance the anti-tumor activity of standard of care therapy in progressing patients. Citation Format: Eleni Farmaki, Rena Emond, Aritro Nath, Vince K. Grolmusz, Patrick A. Cosgrove, Andrea H. Bild. Acquired sensitivity to ONC201/TIC10 in ER+ breast cancer progressing on the mTOR inhibitor everolimus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 388.
Abstract 200: Patient-derived cervical cancer organoids as a pre-clinical model predicting drug and radiation response
Authors: Ju Hee Oh, Hyang Sook Seol, Eun Hye Choi, Yong Jae Lee Lee, Jung-Yun Lee, Sang Wun Kim, Sunghoon Kim, Young Tae Kim, Hyun Ki Kim, Young Joo Lee, Eun Ji Nam
Journal: Cancer Research (2023)

Abstract Objective: Advanced cervical cancer is still difficult to treat and in the case of recurrent cancer, it is desirable to utilize personalized treatment rather than uniform treatment because the type of recurrence is different for each individual. Therefore, this study aimed to establish patients-derived organoid platform to determine the effects of chemotherapy, radiation therapy, and targeted therapy in cervical cancer. Methods: We established organoids from four patients with various types of cervical cancer. The histopathological and gene profiles of these organoid models were compared to determine their characteristics and the maintenance of the patient phenotype. Each type of organoid was also subjected to anticancer drug screening and radiation therapy to evaluate its sensitivity. Results: We established patient-derived organoids recapitulated the main elements of the original patient tumors, including the DNA copy number and mutational profile. We screened seven drugs that showed growth inhibition in cervical cancer organoids using two analytical tools (individual drugs and an FDA-approved drug library). Moreover, squamous cell carcinoma and villoglandular carcinoma showed significant response to radiation therapy, however, adenocarcinoma and large-cell neuroendocrine carcinoma showed relative resistance to radiation therapy. Conclusion: Our results showed patient-derived cervical cancer organoid can be used as a pre-clinical model for drug and radiation sensitivity test. These findings suggest that patient-derived cervical cancer organoids could be used as a personalized medicine confirmation tool and to improve treatment options for patients with various subtypes of cervical cancer. Citation Format: Ju Hee Oh, Hyang Sook Seol, Eun Hye Choi, Yong Jae Lee Lee, Jung-Yun Lee, Sang Wun Kim, Sunghoon Kim, Young Tae Kim, Hyun Ki Kim, Young Joo Lee, Eun Ji Nam. Patient-derived cervical cancer organoids as a pre-clinical model predicting drug and radiation response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 200.
Abstract 4556: Matrix properties regulate 3D tumor spheroid growth and cancer drug response
Authors: Jaxson R. Libby, Linqing Li, Sarah R. Walker
Journal: Cancer Research (2023)

Abstract 3D cancer spheroids are vital in vitro models for cancer drug discovery. The current cancer spheroid generation utilizes low-adhesion plates or forced aggregation of single cells. However, certain cancers do not form stable spheroids in these protocols, nor do pre-formed tumor spheroids recapitulate in vivo development and progression. This project aims to overcome this limitation with the use of a biomimetic hydrogel system to mimic in vivo cancer cell growth and tumor development and use it as an in vitro platform for 3D cancer drug screening. The biocompatible and tunable hydrogel permits independent control of key biochemical and biophysical cues such as matrix degradation, cell adhesion, and stiffness; leading to systematic investigation of matrix parameter contribution to regulating in vitro tumor growth and treatment response. We modified a homo-polysaccharide dextran with methacrylate groups and generated dextran macromers (Dex-MA) containing ample reactive methacrylates per polymer. Cell adhesion is mediated by thiol-terminated RGD peptide added to the methacrylates, followed by crosslinking with di-thiolated MMP-labile peptides through Michael-type addition reaction. Varying the sequence of the crosslinker furthermore gives access to a range of degradability, independent of matrix stiffness. Our experiments showed that Dex-MA supported robust growth of SK-BR-3 breast cancer cells from single cell to 3D tumor spheroids, whereas the cell line failed to form tumor aggregates in low-adhesion plates. Alteration of hydrogel stiffness further revealed stiffness dependence of tumor growth, invasion, and response to treatment, suggesting the importance of matrix properties on regulating cell behavior. This dextran-based tunable hydrogel system provides key insights into how engineered matrix properties control tumor growth, critical for screening novel therapy compounds, and may reveal mechanisms for 3D tumor development, invasion, metastasis, and drug resistance. Citation Format: Jaxson R. Libby, Linqing Li, Sarah R. Walker. Matrix properties regulate 3D tumor spheroid growth and cancer drug response. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4556.
Abstract 5791: Autophagy &amp; PIM1 kinase inhibition in breast cancer stem cells &amp; bulk cancer cells attenuates breast cancer &amp; metastasis
Authors: Kanakaraju Manupati, Mingang Hao, Michael Haas, Syn Kok Yeo, Jun-Lin Guan
Journal: Cancer Research (2023)

Abstract Autophagy is a self-degradation process, it is essential for growth of heterogenous of breast cancer cells. Breast tumor heterogeneity majorly comprises bulk cancer cells &amp; cancer stem cells (CSCs). Targeting either CSCs or cancer cells could lead to interconversion between these cells due to EMT/MET transitions. Therefore, it is important to identify a common molecular targets &amp; its mechanism of regulation in these populations for improvement of breast cancer therapy. Here, we utilized a PCR based screen &amp; identified NUMA1 downregulation in FIP200 KO (autophagy gene) cells of three major breast cancer subtypes, FF99 (luminal), N418 (Her2+) &amp; BF3M (basal). Further, NUMA1 KO in these cells reduced tumor formation &amp; CSCs indicating the role of NUMA1 on regulation of CSCs. Therefore, we sorted breast CSCs, ALDH+ and CD29hi CD61+ from WT &amp; NUMA1 KO cells, tail-vein injected nude mice depicted reduced metastatic potential with NUMA1 KO than WT CSCs. Mechanistically, NUMA1 regulation by PIM1 kinase was observed in CSCs but not in bulk cancer cells. Cell viability assays revealed that combination treatment of autophagy &amp; PIM1 inhibitor showed higher efficacy against cancer cells of three breast cancer subtypes than individual treatments alone. Finally, the combination treatment of autophagy inhibitor, Lys05 &amp; PIM1 inhibitor, SMI-4a reduced tumor formation &amp; metastasis of breast cancer. Human tissue microarray results depicted high expression of NUMA1 &amp; PIM1 in different breast cancer subtypes than non- tumor tissues. Our study demonstrated that inhibition of autophagy &amp; PIM1 in bulk cancer cells &amp; CSCs showed attenuation of tumor formation &amp; metastasis, suggesting this combination treatment serves as an important therapeutic approach for treating breast cancer. Citation Format: Kanakaraju Manupati, Mingang Hao, Michael Haas, Syn Kok Yeo, Jun-Lin Guan. Autophagy &amp; PIM1 kinase inhibition in breast cancer stem cells &amp; bulk cancer cells attenuates breast cancer &amp; metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5791.
Abstract 5800: Anti-metastatic potential of pitavastatin in triple-negative breast cancer via targeting breast cancer stem-like properties and STAT3 signaling
Authors: Dongmi Ko, Juyeon Seo, Seongjae Kim, Soeun Park, Minsu Park, Kee Dal Nam, Yong koo Kang, Sora Seock, Eunsun Jung, Yoon-Jae Kim, Jaeyoun Park, Ji Young Kim, Jae Hong Seo
Journal: Cancer Research (2023)

Abstract Triple-negative breast cancer (TNBC) is the most deadly and aggressive phenotype, with a higher rate of metastatic recurrence. TNBC does yet have a suitable treatment option other than cytotoxic anticancer drugs. Although pitavastatin has been shown to exert anti-proliferative effects and cytotoxicity in various types of cancer cells, the precise mechanisms underlying pitavastatin’s anti-cancer effects in TNBC have not been fully elucidated. We sought to investigate the mechanism of pitavastatin-induced apoptosis and its effects on cancer stem cell (CSC)-like characteristics in TNBC. Exposure to pitavastatin induced mitochondria-mediated apoptotic cell death in BT549 and 4T1 cells. Mitochondrial dysfunction was accompanied with a robust production of reactive oxygen species (ROS) and collapse of mitochondrial membrane potential (MMP), resulting in subsequent activation of caspase-3/-7 and PARP cleavage. Pitavastatin effectively suppressed CSC-like properties in TNBC via targeting CD44+/CD24- and CD49f+/CD24- phenotypes, as well as impediment of mammosphere formation in vitro. This phenomenon was accompanied with dysregulation of STAT3 survival pathway, concomitant with significant downregulation of cyclin D1, survivin and vimentin. Pitavastatin effectively targets both the proliferating TNBC tumor cells and CSCs via the dysregulation of STAT3 and suppression of CSC-like properties, markedly reducing angiogenesis and tumor growth, coinciding with decreased Ki-67 expression. It is noteworthy that pitavastatin considerably suppressed metastasis, coinciding with significant reduction of MMP-2, MMP-9 and VEGF in the circulating blood of mice. Our findings highlight that pitavastatin may be potentially effective for the treatment of metastatic TNBC. Citation Format: Dongmi Ko, Juyeon Seo, Seongjae Kim, Soeun Park, Minsu Park, Kee Dal Nam, Yong koo Kang, Sora Seock, Eunsun Jung, Yoon-Jae Kim, Jaeyoun Park, Ji Young Kim, Jae Hong Seo. Anti-metastatic potential of pitavastatin in triple-negative breast cancer via targeting breast cancer stem-like properties and STAT3 signaling. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5800.